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TASK-2095 - Duplicated libraries at opencga/build/libs #250

Merged
merged 13 commits into from
Nov 13, 2023
Merged

TASK-2095 - Duplicated libraries at opencga/build/libs #250

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73ab330
Prepare next release 2.7.2-SNAPSHOT
juanfeSanahuja Mar 23, 2023
0ad483c
Prepare new development branch release-2.8.x
juanfeSanahuja Apr 19, 2023
4a8bc8f
pom:several dependency cleanups #TASK-2095
juanfeSanahuja May 4, 2023
fa0f873
pom: Dependency cleanups #TASK-2095
juanfeSanahuja May 4, 2023
02d8e7f
pom: minor style changes
imedina May 5, 2023
eeac691
Merge branch 'release-2.8.x' into TASK-2095
imedina May 5, 2023
28e5e45
pom: minor style changes
imedina May 5, 2023
6555f52
pm: downgrade guava to 22.0
imedina May 5, 2023
bfb4ec5
clean pom TASK-2095
juanfeSanahuja Oct 11, 2023
4ad3889
Merge branch 'develop' into TASK-2095
juanfeSanahuja Oct 11, 2023
e518408
pom: upgrade dependency plugin version
imedina Oct 13, 2023
d0f7d6e
pom: Added develop dependencies to review #TASK-2095
juanfeSanahuja Oct 19, 2023
ea6f66e
Merge branch 'develop' into TASK-2095
juanfeSanahuja Nov 13, 2023
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5 changes: 5 additions & 0 deletions biodata-external/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,11 @@
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<!--TODO Review -->
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
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49 changes: 46 additions & 3 deletions biodata-formats/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,28 +34,71 @@
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-models</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
</dependency>

<dependency>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>2.3.3</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.3.3</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-oboformat</artifactId>
<version>5.1.13</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<!--TODO Review -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
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30 changes: 27 additions & 3 deletions biodata-models/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,14 @@
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>

<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
Expand All @@ -56,14 +59,35 @@
<artifactId>protobuf-java</artifactId>
</dependency>
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-all</artifactId>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<!--TODO Review -->
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-all</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
Expand Down
97 changes: 72 additions & 25 deletions biodata-tools/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,51 +34,92 @@
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-models</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.ga4gh</groupId>
<artifactId>ga4gh</artifactId>
<version>0.6.0a5</version>
<exclusions>
<exclusion>
<groupId>org.apache.avro</groupId>
<artifactId>avro-ipc</artifactId>
</exclusion>
</exclusions>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
</dependency>

<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
<groupId>org.opencb.ga4gh</groupId>
<artifactId>ga4gh</artifactId>
</dependency>
<dependency>
<groupId>com.databricks</groupId>
<artifactId>SnpEff</artifactId>
<version>4.3.1</version>
<exclusions>
<exclusion>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</exclusion>
<exclusion>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.rocksdb</groupId>
<artifactId>rocksdbjni</artifactId>
<version>4.5.1</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
</dependency>
<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</dependency>
<!--TEST-->
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-models</artifactId>
Expand All @@ -91,6 +132,12 @@
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>

<!--TODO Review -->
<dependency>
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Pretty sure this one is not needed...
b839ae1

<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
Expand Down
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